Note
Click here to download the full example code
RecoBundles80 using AFQ API¶
An example using the AFQ API to run recobundles with the 80 bundle atlas.
import os.path as op
import plotly
from AFQ import api
import AFQ.data as afd
Get some example data¶
Retrieves Stanford HARDI dataset.
afd.organize_stanford_data(clear_previous_afq=True)
Out:
0%| | 0/5578 [00:00<?, ? MB/s]
0%| | 3/5578 [00:00<04:41, 19.79 MB/s]
0%| | 6/5578 [00:00<04:41, 19.78 MB/s]
0%| | 11/5578 [00:00<03:35, 25.82 MB/s]
0%| | 17/5578 [00:00<02:57, 31.39 MB/s]
0%| | 26/5578 [00:00<02:13, 41.47 MB/s]
1%| | 36/5578 [00:00<01:51, 49.87 MB/s]
1%| | 49/5578 [00:01<01:29, 61.57 MB/s]
1%|1 | 65/5578 [00:01<01:12, 75.59 MB/s]
1%|1 | 81/5578 [00:01<01:04, 84.88 MB/s]
2%|1 | 97/5578 [00:01<00:59, 91.37 MB/s]
2%|2 | 113/5578 [00:01<00:57, 95.72 MB/s]
2%|2 | 128/5578 [00:01<00:56, 96.66 MB/s]
3%|2 | 144/5578 [00:01<00:54, 99.33 MB/s]
3%|2 | 160/5578 [00:02<00:53, 101.27 MB/s]
3%|3 | 176/5578 [00:02<00:52, 102.21 MB/s]
3%|3 | 192/5578 [00:02<00:52, 103.14 MB/s]
4%|3 | 208/5578 [00:02<00:51, 103.57 MB/s]
4%|4 | 224/5578 [00:02<00:51, 104.15 MB/s]
4%|4 | 240/5578 [00:02<00:51, 103.77 MB/s]
5%|4 | 256/5578 [00:03<00:51, 104.18 MB/s]
5%|4 | 271/5578 [00:03<00:51, 102.69 MB/s]
5%|5 | 287/5578 [00:03<00:51, 103.49 MB/s]
5%|5 | 303/5578 [00:03<00:50, 104.01 MB/s]
6%|5 | 319/5578 [00:03<00:50, 103.91 MB/s]
6%|6 | 335/5578 [00:03<00:50, 104.42 MB/s]
6%|6 | 351/5578 [00:03<00:50, 103.30 MB/s]
7%|6 | 367/5578 [00:04<00:50, 103.86 MB/s]
7%|6 | 383/5578 [00:04<00:49, 104.30 MB/s]
7%|7 | 399/5578 [00:04<00:49, 104.68 MB/s]
7%|7 | 415/5578 [00:04<00:49, 105.05 MB/s]
8%|7 | 430/5578 [00:04<00:46, 109.79 MB/s]
8%|7 | 442/5578 [00:04<00:46, 109.87 MB/s]
8%|8 | 454/5578 [00:04<00:51, 100.05 MB/s]
8%|8 | 470/5578 [00:05<00:50, 101.85 MB/s]
9%|8 | 486/5578 [00:05<00:49, 102.97 MB/s]
9%|8 | 502/5578 [00:05<00:48, 103.71 MB/s]
9%|9 | 518/5578 [00:05<00:48, 104.28 MB/s]
10%|9 | 534/5578 [00:05<00:48, 104.60 MB/s]
10%|9 | 550/5578 [00:05<00:47, 104.91 MB/s]
10%|# | 566/5578 [00:06<00:48, 104.16 MB/s]
10%|# | 581/5578 [00:06<00:48, 102.58 MB/s]
11%|# | 597/5578 [00:06<00:48, 103.57 MB/s]
11%|# | 613/5578 [00:06<00:47, 104.17 MB/s]
11%|#1 | 629/5578 [00:06<00:47, 104.30 MB/s]
12%|#1 | 645/5578 [00:06<00:47, 104.79 MB/s]
12%|#1 | 661/5578 [00:06<00:46, 105.03 MB/s]
12%|#2 | 677/5578 [00:07<00:46, 105.11 MB/s]
12%|#2 | 693/5578 [00:07<00:46, 105.26 MB/s]
13%|#2 | 708/5578 [00:07<00:47, 103.46 MB/s]
13%|#2 | 724/5578 [00:07<00:46, 104.14 MB/s]
13%|#3 | 740/5578 [00:07<00:46, 104.55 MB/s]
14%|#3 | 756/5578 [00:07<00:46, 104.80 MB/s]
14%|#3 | 772/5578 [00:07<00:45, 105.12 MB/s]
14%|#4 | 788/5578 [00:08<00:45, 105.18 MB/s]
14%|#4 | 804/5578 [00:08<00:45, 105.25 MB/s]
15%|#4 | 820/5578 [00:08<00:45, 105.33 MB/s]
15%|#4 | 835/5578 [00:08<00:45, 103.47 MB/s]
15%|#5 | 851/5578 [00:08<00:45, 104.08 MB/s]
16%|#5 | 867/5578 [00:08<00:45, 104.55 MB/s]
16%|#5 | 883/5578 [00:09<00:44, 104.66 MB/s]
16%|#6 | 899/5578 [00:09<00:44, 104.80 MB/s]
16%|#6 | 915/5578 [00:09<00:44, 104.97 MB/s]
17%|#6 | 931/5578 [00:09<00:44, 105.03 MB/s]
17%|#6 | 947/5578 [00:09<00:44, 105.20 MB/s]
17%|#7 | 962/5578 [00:09<00:44, 103.42 MB/s]
18%|#7 | 978/5578 [00:09<00:44, 104.12 MB/s]
18%|#7 | 994/5578 [00:10<00:43, 104.44 MB/s]
18%|#8 | 1010/5578 [00:10<00:43, 104.65 MB/s]
18%|#8 | 1026/5578 [00:10<00:43, 104.96 MB/s]
19%|#8 | 1042/5578 [00:10<00:43, 105.18 MB/s]
19%|#8 | 1058/5578 [00:10<00:42, 105.22 MB/s]
19%|#9 | 1074/5578 [00:10<00:42, 105.30 MB/s]
20%|#9 | 1090/5578 [00:11<00:42, 105.31 MB/s]
20%|#9 | 1105/5578 [00:11<00:43, 103.42 MB/s]
20%|## | 1121/5578 [00:11<00:42, 104.03 MB/s]
20%|## | 1137/5578 [00:11<00:42, 104.22 MB/s]
21%|## | 1153/5578 [00:11<00:42, 104.50 MB/s]
21%|## | 1169/5578 [00:11<00:42, 104.58 MB/s]
21%|##1 | 1185/5578 [00:11<00:41, 104.92 MB/s]
22%|##1 | 1201/5578 [00:12<00:41, 105.18 MB/s]
22%|##1 | 1217/5578 [00:12<00:41, 105.35 MB/s]
22%|##2 | 1232/5578 [00:12<00:42, 103.31 MB/s]
22%|##2 | 1248/5578 [00:12<00:41, 103.95 MB/s]
23%|##2 | 1264/5578 [00:12<00:41, 104.50 MB/s]
23%|##2 | 1280/5578 [00:12<00:41, 104.83 MB/s]
23%|##3 | 1296/5578 [00:12<00:40, 105.09 MB/s]
24%|##3 | 1312/5578 [00:13<00:40, 105.22 MB/s]
24%|##3 | 1328/5578 [00:13<00:40, 105.38 MB/s]
24%|##4 | 1343/5578 [00:13<00:40, 103.37 MB/s]
24%|##4 | 1359/5578 [00:13<00:40, 103.82 MB/s]
25%|##4 | 1375/5578 [00:13<00:40, 104.40 MB/s]
25%|##4 | 1391/5578 [00:13<00:40, 104.65 MB/s]
25%|##5 | 1407/5578 [00:14<00:39, 104.95 MB/s]
26%|##5 | 1423/5578 [00:14<00:39, 105.04 MB/s]
26%|##5 | 1439/5578 [00:14<00:39, 105.11 MB/s]
26%|##6 | 1455/5578 [00:14<00:39, 105.18 MB/s]
26%|##6 | 1471/5578 [00:14<00:39, 105.16 MB/s]
27%|##6 | 1486/5578 [00:14<00:39, 103.36 MB/s]
27%|##6 | 1502/5578 [00:14<00:39, 103.87 MB/s]
27%|##7 | 1518/5578 [00:15<00:38, 104.26 MB/s]
28%|##7 | 1534/5578 [00:15<00:38, 104.52 MB/s]
28%|##7 | 1550/5578 [00:15<00:38, 104.72 MB/s]
28%|##8 | 1566/5578 [00:15<00:38, 104.99 MB/s]
28%|##8 | 1582/5578 [00:15<00:37, 105.27 MB/s]
29%|##8 | 1597/5578 [00:15<00:38, 103.35 MB/s]
29%|##8 | 1613/5578 [00:16<00:38, 103.69 MB/s]
29%|##9 | 1629/5578 [00:16<00:37, 104.06 MB/s]
29%|##9 | 1645/5578 [00:16<00:37, 104.42 MB/s]
30%|##9 | 1657/5578 [00:16<00:38, 100.97 MB/s]
30%|##9 | 1673/5578 [00:16<00:38, 102.42 MB/s]
30%|### | 1689/5578 [00:16<00:37, 103.22 MB/s]
31%|### | 1705/5578 [00:16<00:37, 103.92 MB/s]
31%|### | 1721/5578 [00:17<00:36, 104.38 MB/s]
31%|###1 | 1737/5578 [00:17<00:36, 104.72 MB/s]
31%|###1 | 1753/5578 [00:17<00:36, 104.86 MB/s]
32%|###1 | 1769/5578 [00:17<00:36, 104.84 MB/s]
32%|###2 | 1785/5578 [00:17<00:36, 105.12 MB/s]
32%|###2 | 1801/5578 [00:17<00:35, 105.24 MB/s]
33%|###2 | 1816/5578 [00:17<00:36, 103.39 MB/s]
33%|###2 | 1832/5578 [00:18<00:36, 103.04 MB/s]
33%|###3 | 1848/5578 [00:18<00:35, 103.78 MB/s]
33%|###3 | 1864/5578 [00:18<00:35, 104.10 MB/s]
34%|###3 | 1880/5578 [00:18<00:35, 104.57 MB/s]
34%|###3 | 1896/5578 [00:18<00:35, 104.82 MB/s]
34%|###4 | 1912/5578 [00:18<00:34, 105.11 MB/s]
35%|###4 | 1928/5578 [00:19<00:34, 105.21 MB/s]
35%|###4 | 1944/5578 [00:19<00:34, 105.26 MB/s]
35%|###5 | 1960/5578 [00:19<00:34, 105.23 MB/s]
35%|###5 | 1975/5578 [00:19<00:34, 103.16 MB/s]
36%|###5 | 1991/5578 [00:19<00:34, 103.94 MB/s]
36%|###5 | 2007/5578 [00:19<00:34, 104.24 MB/s]
36%|###6 | 2023/5578 [00:19<00:33, 104.63 MB/s]
37%|###6 | 2039/5578 [00:20<00:33, 104.87 MB/s]
37%|###6 | 2055/5578 [00:20<00:33, 105.12 MB/s]
37%|###7 | 2071/5578 [00:20<00:33, 105.28 MB/s]
37%|###7 | 2087/5578 [00:20<00:33, 105.51 MB/s]
38%|###7 | 2103/5578 [00:20<00:32, 105.54 MB/s]
38%|###7 | 2119/5578 [00:20<00:32, 105.54 MB/s]
38%|###8 | 2134/5578 [00:21<00:33, 103.38 MB/s]
39%|###8 | 2150/5578 [00:21<00:32, 104.10 MB/s]
39%|###8 | 2166/5578 [00:21<00:32, 104.65 MB/s]
39%|###9 | 2182/5578 [00:21<00:32, 104.95 MB/s]
39%|###9 | 2198/5578 [00:21<00:32, 105.18 MB/s]
40%|###9 | 2214/5578 [00:21<00:31, 105.40 MB/s]
40%|###9 | 2230/5578 [00:21<00:31, 105.44 MB/s]
40%|#### | 2246/5578 [00:22<00:31, 105.32 MB/s]
41%|#### | 2261/5578 [00:22<00:32, 103.53 MB/s]
41%|#### | 2277/5578 [00:22<00:31, 104.17 MB/s]
41%|####1 | 2293/5578 [00:22<00:31, 104.67 MB/s]
41%|####1 | 2309/5578 [00:22<00:31, 104.92 MB/s]
42%|####1 | 2325/5578 [00:22<00:30, 105.22 MB/s]
42%|####1 | 2341/5578 [00:22<00:30, 105.23 MB/s]
42%|####2 | 2357/5578 [00:23<00:30, 105.33 MB/s]
43%|####2 | 2372/5578 [00:23<00:31, 103.33 MB/s]
43%|####2 | 2388/5578 [00:23<00:30, 104.06 MB/s]
43%|####3 | 2404/5578 [00:23<00:30, 104.37 MB/s]
43%|####3 | 2420/5578 [00:23<00:30, 104.68 MB/s]
44%|####3 | 2436/5578 [00:23<00:29, 104.89 MB/s]
44%|####3 | 2452/5578 [00:24<00:29, 104.96 MB/s]
44%|####4 | 2468/5578 [00:24<00:29, 105.20 MB/s]
45%|####4 | 2484/5578 [00:24<00:29, 105.28 MB/s]
45%|####4 | 2499/5578 [00:24<00:29, 103.51 MB/s]
45%|####5 | 2515/5578 [00:24<00:29, 104.02 MB/s]
45%|####5 | 2531/5578 [00:24<00:29, 104.49 MB/s]
46%|####5 | 2547/5578 [00:24<00:28, 104.57 MB/s]
46%|####5 | 2563/5578 [00:25<00:28, 104.93 MB/s]
46%|####6 | 2579/5578 [00:25<00:28, 105.11 MB/s]
47%|####6 | 2595/5578 [00:25<00:28, 104.88 MB/s]
47%|####6 | 2611/5578 [00:25<00:28, 105.12 MB/s]
47%|####7 | 2627/5578 [00:25<00:27, 105.40 MB/s]
47%|####7 | 2642/5578 [00:25<00:28, 103.47 MB/s]
48%|####7 | 2658/5578 [00:26<00:28, 104.02 MB/s]
48%|####7 | 2674/5578 [00:26<00:27, 104.42 MB/s]
48%|####8 | 2690/5578 [00:26<00:27, 104.63 MB/s]
49%|####8 | 2706/5578 [00:26<00:27, 104.72 MB/s]
49%|####8 | 2722/5578 [00:26<00:27, 104.99 MB/s]
49%|####9 | 2738/5578 [00:26<00:27, 104.93 MB/s]
49%|####9 | 2753/5578 [00:26<00:27, 103.23 MB/s]
50%|####9 | 2769/5578 [00:27<00:27, 103.94 MB/s]
50%|####9 | 2785/5578 [00:27<00:26, 104.46 MB/s]
50%|##### | 2801/5578 [00:27<00:26, 104.69 MB/s]
51%|##### | 2817/5578 [00:27<00:26, 104.95 MB/s]
51%|##### | 2833/5578 [00:27<00:26, 105.24 MB/s]
51%|#####1 | 2849/5578 [00:27<00:25, 105.42 MB/s]
51%|#####1 | 2865/5578 [00:27<00:25, 105.48 MB/s]
52%|#####1 | 2880/5578 [00:28<00:26, 103.53 MB/s]
52%|#####1 | 2896/5578 [00:28<00:25, 104.11 MB/s]
52%|#####2 | 2912/5578 [00:28<00:25, 104.71 MB/s]
52%|#####2 | 2928/5578 [00:28<00:25, 105.03 MB/s]
53%|#####2 | 2944/5578 [00:28<00:25, 105.02 MB/s]
53%|#####3 | 2960/5578 [00:28<00:24, 105.13 MB/s]
53%|#####3 | 2976/5578 [00:29<00:24, 105.18 MB/s]
54%|#####3 | 2991/5578 [00:29<00:25, 103.28 MB/s]
54%|#####3 | 3007/5578 [00:29<00:24, 103.99 MB/s]
54%|#####4 | 3023/5578 [00:29<00:24, 104.43 MB/s]
54%|#####4 | 3039/5578 [00:29<00:24, 104.51 MB/s]
55%|#####4 | 3055/5578 [00:29<00:24, 104.85 MB/s]
55%|#####5 | 3071/5578 [00:29<00:23, 105.02 MB/s]
55%|#####5 | 3087/5578 [00:30<00:23, 105.07 MB/s]
56%|#####5 | 3103/5578 [00:30<00:23, 105.14 MB/s]
56%|#####5 | 3118/5578 [00:30<00:23, 103.72 MB/s]
56%|#####6 | 3133/5578 [00:30<00:21, 113.67 MB/s]
56%|#####6 | 3145/5578 [00:30<00:23, 104.89 MB/s]
57%|#####6 | 3158/5578 [00:30<00:23, 102.00 MB/s]
57%|#####6 | 3173/5578 [00:30<00:21, 113.37 MB/s]
57%|#####7 | 3185/5578 [00:31<00:23, 104.00 MB/s]
57%|#####7 | 3198/5578 [00:31<00:23, 100.88 MB/s]
58%|#####7 | 3213/5578 [00:31<00:23, 102.61 MB/s]
58%|#####7 | 3225/5578 [00:31<00:22, 105.34 MB/s]
58%|#####8 | 3237/5578 [00:31<00:23, 101.32 MB/s]
58%|#####8 | 3253/5578 [00:31<00:22, 102.83 MB/s]
59%|#####8 | 3269/5578 [00:31<00:22, 103.72 MB/s]
59%|#####8 | 3285/5578 [00:32<00:21, 104.35 MB/s]
59%|#####9 | 3301/5578 [00:32<00:21, 104.30 MB/s]
59%|#####9 | 3317/5578 [00:32<00:21, 104.75 MB/s]
60%|#####9 | 3332/5578 [00:32<00:21, 103.41 MB/s]
60%|###### | 3348/5578 [00:32<00:21, 104.15 MB/s]
60%|###### | 3364/5578 [00:32<00:21, 104.51 MB/s]
61%|###### | 3380/5578 [00:32<00:20, 104.83 MB/s]
61%|###### | 3396/5578 [00:33<00:20, 104.81 MB/s]
61%|######1 | 3412/5578 [00:33<00:20, 105.09 MB/s]
61%|######1 | 3428/5578 [00:33<00:20, 105.17 MB/s]
62%|######1 | 3443/5578 [00:33<00:20, 103.65 MB/s]
62%|######2 | 3459/5578 [00:33<00:20, 104.27 MB/s]
62%|######2 | 3475/5578 [00:33<00:20, 104.79 MB/s]
63%|######2 | 3491/5578 [00:33<00:19, 105.13 MB/s]
63%|######2 | 3507/5578 [00:34<00:19, 104.84 MB/s]
63%|######3 | 3523/5578 [00:34<00:19, 105.11 MB/s]
63%|######3 | 3539/5578 [00:34<00:19, 105.27 MB/s]
64%|######3 | 3555/5578 [00:34<00:19, 105.34 MB/s]
64%|######4 | 3570/5578 [00:34<00:19, 103.71 MB/s]
64%|######4 | 3586/5578 [00:34<00:19, 104.29 MB/s]
65%|######4 | 3602/5578 [00:35<00:18, 104.64 MB/s]
65%|######4 | 3618/5578 [00:35<00:18, 105.03 MB/s]
65%|######5 | 3634/5578 [00:35<00:18, 105.25 MB/s]
65%|######5 | 3650/5578 [00:35<00:18, 104.65 MB/s]
66%|######5 | 3666/5578 [00:35<00:18, 104.78 MB/s]
66%|######6 | 3682/5578 [00:35<00:18, 105.01 MB/s]
66%|######6 | 3697/5578 [00:35<00:18, 103.18 MB/s]
67%|######6 | 3713/5578 [00:36<00:17, 103.76 MB/s]
67%|######6 | 3729/5578 [00:36<00:17, 104.23 MB/s]
67%|######7 | 3745/5578 [00:36<00:17, 104.58 MB/s]
67%|######7 | 3761/5578 [00:36<00:17, 104.82 MB/s]
68%|######7 | 3777/5578 [00:36<00:17, 104.70 MB/s]
68%|######7 | 3793/5578 [00:36<00:17, 104.77 MB/s]
68%|######8 | 3809/5578 [00:37<00:16, 105.00 MB/s]
69%|######8 | 3824/5578 [00:37<00:16, 103.87 MB/s]
69%|######8 | 3840/5578 [00:37<00:16, 104.13 MB/s]
69%|######9 | 3856/5578 [00:37<00:16, 104.82 MB/s]
69%|######9 | 3872/5578 [00:37<00:16, 105.18 MB/s]
70%|######9 | 3884/5578 [00:37<00:15, 108.34 MB/s]
70%|######9 | 3896/5578 [00:37<00:16, 103.32 MB/s]
70%|####### | 3912/5578 [00:38<00:16, 104.06 MB/s]
70%|####### | 3927/5578 [00:38<00:15, 103.50 MB/s]
71%|####### | 3940/5578 [00:38<00:14, 109.49 MB/s]
71%|####### | 3952/5578 [00:38<00:15, 104.02 MB/s]
71%|#######1 | 3967/5578 [00:38<00:15, 103.36 MB/s]
71%|#######1 | 3979/5578 [00:38<00:14, 107.03 MB/s]
72%|#######1 | 3991/5578 [00:38<00:15, 102.19 MB/s]
72%|#######1 | 4007/5578 [00:38<00:15, 103.14 MB/s]
72%|#######2 | 4023/5578 [00:39<00:14, 103.89 MB/s]
72%|#######2 | 4039/5578 [00:39<00:14, 104.41 MB/s]
73%|#######2 | 4054/5578 [00:39<00:14, 104.05 MB/s]
73%|#######2 | 4066/5578 [00:39<00:14, 106.62 MB/s]
73%|#######3 | 4078/5578 [00:39<00:14, 103.91 MB/s]
73%|#######3 | 4090/5578 [00:39<00:13, 106.73 MB/s]
74%|#######3 | 4102/5578 [00:39<00:14, 102.82 MB/s]
74%|#######3 | 4116/5578 [00:39<00:13, 112.37 MB/s]
74%|#######4 | 4128/5578 [00:40<00:13, 106.15 MB/s]
74%|#######4 | 4142/5578 [00:40<00:14, 101.68 MB/s]
74%|#######4 | 4154/5578 [00:40<00:13, 106.17 MB/s]
75%|#######4 | 4166/5578 [00:40<00:13, 102.45 MB/s]
75%|#######4 | 4177/5578 [00:40<00:13, 104.19 MB/s]
75%|#######5 | 4189/5578 [00:40<00:13, 102.31 MB/s]
75%|#######5 | 4201/5578 [00:40<00:13, 105.72 MB/s]
76%|#######5 | 4213/5578 [00:40<00:13, 102.09 MB/s]
76%|#######5 | 4225/5578 [00:40<00:12, 106.84 MB/s]
76%|#######5 | 4237/5578 [00:41<00:13, 102.83 MB/s]
76%|#######6 | 4249/5578 [00:41<00:12, 107.27 MB/s]
76%|#######6 | 4261/5578 [00:41<00:12, 103.17 MB/s]
77%|#######6 | 4273/5578 [00:41<00:12, 107.48 MB/s]
77%|#######6 | 4285/5578 [00:41<00:12, 102.93 MB/s]
77%|#######7 | 4298/5578 [00:41<00:11, 109.77 MB/s]
77%|#######7 | 4310/5578 [00:41<00:12, 104.21 MB/s]
78%|#######7 | 4324/5578 [00:41<00:11, 113.09 MB/s]
78%|#######7 | 4336/5578 [00:42<00:12, 101.70 MB/s]
78%|#######7 | 4348/5578 [00:42<00:12, 99.21 MB/s]
78%|#######8 | 4362/5578 [00:42<00:11, 109.53 MB/s]
78%|#######8 | 4374/5578 [00:42<00:11, 104.04 MB/s]
79%|#######8 | 4388/5578 [00:42<00:11, 100.49 MB/s]
79%|#######8 | 4401/5578 [00:42<00:10, 107.75 MB/s]
79%|#######9 | 4413/5578 [00:42<00:11, 102.99 MB/s]
79%|#######9 | 4428/5578 [00:42<00:11, 102.19 MB/s]
80%|#######9 | 4441/5578 [00:43<00:10, 109.01 MB/s]
80%|#######9 | 4453/5578 [00:43<00:10, 103.81 MB/s]
80%|######## | 4467/5578 [00:43<00:11, 100.65 MB/s]
80%|######## | 4480/5578 [00:43<00:10, 107.84 MB/s]
81%|######## | 4492/5578 [00:43<00:10, 103.64 MB/s]
81%|######## | 4506/5578 [00:43<00:09, 112.98 MB/s]
81%|######## | 4518/5578 [00:43<00:10, 101.48 MB/s]
81%|########1 | 4531/5578 [00:43<00:10, 100.87 MB/s]
81%|########1 | 4545/5578 [00:44<00:09, 110.69 MB/s]
82%|########1 | 4557/5578 [00:44<00:09, 104.88 MB/s]
82%|########1 | 4570/5578 [00:44<00:10, 98.87 MB/s]
82%|########2 | 4586/5578 [00:44<00:09, 101.04 MB/s]
83%|########2 | 4602/5578 [00:44<00:09, 102.46 MB/s]
83%|########2 | 4618/5578 [00:44<00:09, 103.37 MB/s]
83%|########3 | 4634/5578 [00:44<00:09, 103.97 MB/s]
83%|########3 | 4650/5578 [00:45<00:08, 104.33 MB/s]
84%|########3 | 4665/5578 [00:45<00:08, 105.25 MB/s]
84%|########3 | 4677/5578 [00:45<00:08, 106.80 MB/s]
84%|########4 | 4689/5578 [00:45<00:08, 102.05 MB/s]
84%|########4 | 4705/5578 [00:45<00:08, 103.19 MB/s]
85%|########4 | 4721/5578 [00:45<00:08, 104.04 MB/s]
85%|########4 | 4737/5578 [00:45<00:08, 104.19 MB/s]
85%|########5 | 4753/5578 [00:46<00:07, 104.54 MB/s]
85%|########5 | 4769/5578 [00:46<00:07, 104.79 MB/s]
86%|########5 | 4785/5578 [00:46<00:07, 105.04 MB/s]
86%|########6 | 4800/5578 [00:46<00:07, 106.13 MB/s]
86%|########6 | 4812/5578 [00:46<00:07, 106.53 MB/s]
86%|########6 | 4824/5578 [00:46<00:07, 102.90 MB/s]
87%|########6 | 4837/5578 [00:46<00:06, 109.34 MB/s]
87%|########6 | 4849/5578 [00:46<00:06, 104.33 MB/s]
87%|########7 | 4864/5578 [00:47<00:06, 102.55 MB/s]
87%|########7 | 4880/5578 [00:47<00:06, 103.41 MB/s]
88%|########7 | 4896/5578 [00:47<00:06, 104.12 MB/s]
88%|########8 | 4912/5578 [00:47<00:06, 104.60 MB/s]
88%|########8 | 4927/5578 [00:47<00:06, 102.94 MB/s]
89%|########8 | 4943/5578 [00:47<00:06, 103.70 MB/s]
89%|########8 | 4959/5578 [00:48<00:05, 104.26 MB/s]
89%|########9 | 4975/5578 [00:48<00:05, 104.75 MB/s]
89%|########9 | 4988/5578 [00:48<00:05, 110.28 MB/s]
90%|########9 | 5000/5578 [00:48<00:05, 105.55 MB/s]
90%|########9 | 5013/5578 [00:48<00:05, 111.50 MB/s]
90%|######### | 5025/5578 [00:48<00:05, 106.02 MB/s]
90%|######### | 5038/5578 [00:48<00:05, 99.49 MB/s]
91%|######### | 5053/5578 [00:48<00:04, 111.48 MB/s]
91%|######### | 5065/5578 [00:49<00:04, 105.68 MB/s]
91%|#########1| 5078/5578 [00:49<00:05, 99.56 MB/s]
91%|#########1| 5093/5578 [00:49<00:04, 111.84 MB/s]
92%|#########1| 5105/5578 [00:49<00:04, 105.88 MB/s]
92%|#########1| 5118/5578 [00:49<00:04, 99.28 MB/s]
92%|#########1| 5131/5578 [00:49<00:04, 106.79 MB/s]
92%|#########2| 5143/5578 [00:49<00:04, 102.85 MB/s]
92%|#########2| 5154/5578 [00:49<00:04, 104.48 MB/s]
93%|#########2| 5165/5578 [00:49<00:04, 98.94 MB/s]
93%|#########2| 5177/5578 [00:50<00:03, 104.11 MB/s]
93%|#########3| 5189/5578 [00:50<00:03, 101.09 MB/s]
93%|#########3| 5201/5578 [00:50<00:03, 105.83 MB/s]
93%|#########3| 5213/5578 [00:50<00:03, 102.25 MB/s]
94%|#########3| 5225/5578 [00:50<00:03, 106.79 MB/s]
94%|#########3| 5237/5578 [00:50<00:03, 102.93 MB/s]
94%|#########4| 5249/5578 [00:50<00:03, 107.41 MB/s]
94%|#########4| 5260/5578 [00:50<00:03, 100.48 MB/s]
95%|#########4| 5272/5578 [00:51<00:02, 105.35 MB/s]
95%|#########4| 5284/5578 [00:51<00:02, 101.91 MB/s]
95%|#########4| 5296/5578 [00:51<00:02, 106.52 MB/s]
95%|#########5| 5308/5578 [00:51<00:02, 102.60 MB/s]
95%|#########5| 5320/5578 [00:51<00:02, 107.05 MB/s]
96%|#########5| 5332/5578 [00:51<00:02, 102.77 MB/s]
96%|#########5| 5344/5578 [00:51<00:02, 107.04 MB/s]
96%|#########6| 5356/5578 [00:51<00:02, 103.21 MB/s]
96%|#########6| 5368/5578 [00:51<00:01, 107.41 MB/s]
96%|#########6| 5379/5578 [00:52<00:01, 100.73 MB/s]
97%|#########6| 5391/5578 [00:52<00:01, 105.45 MB/s]
97%|#########6| 5403/5578 [00:52<00:01, 102.19 MB/s]
97%|#########7| 5415/5578 [00:52<00:01, 106.56 MB/s]
97%|#########7| 5427/5578 [00:52<00:01, 102.95 MB/s]
98%|#########7| 5439/5578 [00:52<00:01, 106.54 MB/s]
98%|#########7| 5451/5578 [00:52<00:01, 103.38 MB/s]
98%|#########7| 5463/5578 [00:52<00:01, 106.84 MB/s]
98%|#########8| 5475/5578 [00:52<00:00, 103.55 MB/s]
98%|#########8| 5487/5578 [00:53<00:00, 106.95 MB/s]
99%|#########8| 5498/5578 [00:53<00:00, 101.03 MB/s]
99%|#########8| 5510/5578 [00:53<00:00, 105.24 MB/s]
99%|#########8| 5522/5578 [00:53<00:00, 102.32 MB/s]
99%|#########9| 5534/5578 [00:53<00:00, 106.40 MB/s]
99%|#########9| 5546/5578 [00:53<00:00, 102.13 MB/s]
100%|#########9| 5560/5578 [00:53<00:00, 112.24 MB/s]
100%|#########9| 5572/5578 [00:53<00:00, 105.96 MB/s]
100%|##########| 5578/5578 [00:53<00:00, 103.51 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2157.56 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3248.88 MB/s]
0%| | 0/71 [00:00<?, ? MB/s]
4%|4 | 3/71 [00:00<00:03, 19.60 MB/s]
8%|8 | 6/71 [00:00<00:03, 19.82 MB/s]
15%|#5 | 11/71 [00:00<00:02, 25.85 MB/s]
25%|##5 | 18/71 [00:00<00:01, 33.75 MB/s]
37%|###6 | 26/71 [00:00<00:01, 40.56 MB/s]
51%|##### | 36/71 [00:00<00:00, 49.09 MB/s]
66%|######6 | 47/71 [00:01<00:00, 56.74 MB/s]
86%|########5 | 61/71 [00:01<00:00, 68.08 MB/s]
100%|##########| 71/71 [00:01<00:00, 54.95 MB/s]
0%| | 0/4 [00:00<?, ? MB/s]
100%|##########| 4/4 [00:00<00:00, 2237.56 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2636.27 MB/s]
Set tractography parameters (optional)¶
We make this tracking_params which we will pass to the AFQ object which specifies that we want 50,000 seeds randomly distributed in the white matter.
We only do this to make this example faster and consume less space.
tracking_params = dict(n_seeds=50000,
random_seeds=True,
rng_seed=42)
Initialize an AFQ object:¶
We specify seg_algo as reco80 in segmentation_params. This tells the AFQ object to perform RecoBundles using the 80 bundles atlas in the segmentation step.
myafq = api.AFQ(bids_path=op.join(afd.afq_home,
'stanford_hardi'),
preproc_pipeline='vistasoft',
segmentation_params={"seg_algo": "reco80"},
tracking_params=tracking_params)
Out:
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
0%| | 0.00/13.4k [00:00<?, ?B/s]
16%|#5 | 2.12k/13.4k [00:00<00:00, 21.2kB/s]
47%|####6 | 6.26k/13.4k [00:00<00:00, 33.1kB/s]
79%|#######8 | 10.5k/13.4k [00:00<00:00, 37.4kB/s]
13.4kB [00:00, 34.3kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
0%| | 0.00/155 [00:00<?, ?B/s]
156B [00:00, 11.0kB/s]
Visualizing bundles and tract profiles:¶
This would run the script and visualize the bundles using the plotly interactive visualization, which should automatically open in a new browser window.
bundle_html = myafq.all_bundles_figure
plotly.io.show(bundle_html["01"])